<tool id="Detect_SNPs_docker" name="Detect_SNPs">
        <description> Detect SNPs  </description>
	<requirements>
	    <container type="docker">takakoron/detect_snp</container>
	</requirements>
	<command interpreter="perl">
		/usr/src/myapp/kick_detect_snps.pl  $how.how_specify

		#if $how.how_specify == "pileup":
			$how.pileup
			$how.consensus
			$how.snp
			$how.map
			$how.coverage
			$how.het_hom_both
			$output1
		#else:
			$how.mpileup
			$how.dp
			$how.mq
			$how.het_hom_both
			$how.gq
			$output1
		#end if
	</command>

	<inputs>
		<conditional name="how">
			<param name="how_specify" type="select" label="Select pileup or mpileup " >
				<option value="mpileup">mpileup</option>
				<option value="pileup">pileup</option>
			</param>
			<when value="pileup">
				<param name="pileup" type="data" label="Select DNA polymorphism file(format : samtools pileup)" />
				<param name="consensus"   area="true"  type="integer" size="1x10" value="0"  label="Consensus quality threshold in pileup file (default: 0)" />
				<param name="snp"   area="true"  type="integer" size="1x10" value="20"  label="SNP quality threshold in pileup file (default: 20)" />
				<param name="map"   area="true"  type="integer" size="1x10" value="0"  label="Maximum mapping quality threshold in pileup file (default: 0)" />
				<param name="coverage"   area="true"  type="integer" size="1x10" value="8"  label="read coverage threshold in pileup file (default: 8)" />
                                <param name="het_hom_both" type="select" label="Select hets, homs or both (default: both)" >
                                        <option value="both">both</option>
                                        <option value="homs">homs</option>
                                        <option value="hets">hets</option>
                                </param>
			</when>
			<when value="mpileup">
				<param name="mpileup" type="data"  label="Select DNA polymorphism file(format : samtools mpileup)" />
				<param name="dp"   area="true"  type="integer" size="1x10" value="0"  label="(DP) Raw read depth threshold in mpileup file (default: 0)" />
				<param name="mq"   area="true"  type="integer" size="1x10" value="0"  label="(MQ) Root-mean-square mapping quality threshold in mpileup file (default: 0)" />
				<param name="het_hom_both" type="select" label="(GT) Select hets, homs or both (default: both)" >
					<option value="both">both</option>
					<option value="homs">homs</option>
					<option value="hets">hets</option>
				</param>
				<param name="gq"   area="true"  type="integer" size="1x10" value="0"  label="(GQ) Genotype quality threshold in mpileup file (default: 0)" />
			</when>
		</conditional>
	</inputs>

	<outputs>
		<data name="output1" label="SNPs data" type="data"  format="vcf"/>
	</outputs>

<!---
   <help>

.. class:: infomark
**About data**

Distribution of chromosome is appeared in order of genome file.

   </help>
-->

</tool>